Exactly. It's just a poor idea. There's too much there between Tony and Jarvis. Even after Jarvitron is defeated, in Avengers 2, there's Avengers 3. Not only should Ultron NEVER go away, but it would be weird to have Tony in the suit in avengers 3 without Jarvis. And if it were the case, and all was good willy nilly, it would be weird, seeing Tony use Jarvis, post Ultron. Was never going to work.

Yeah, Stark would've definitely taken Jarvis offline permanently rather than risk his lifeline AI going rogue again. Strongly doubt anybody wanted to see Jarvis "die," which he most certainly would have in a "Jarvis becomes Ultron" scenario.